Summary information

PDB id
7ntu
Class
hydrolase
Method
X-ray (3.1 Å)
Summary
X-ray structure of the complex between human alpha thrombin and two duplex-quadruplex aptamers: nu172 and hd22_27mer
Reference
Troisi R, Balasco N, Santamaria A, Vitagliano L, Sica F (2021): "Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human alpha-thrombin." Int.J.Biol.Macromol., 181, 858-867. doi: 10.1016/j.ijbiomac.2021.04.076.
Abstract
The long-range communication between the two exosites of human α-thrombin (thrombin) tightly modulates the protein-effector interactions. Duplex/quadruplex aptamers represent an emerging class of very effective binders of thrombin. Among them, NU172 and HD22 aptamers are at the forefront of exosite I and II recognition, respectively. The present study investigates the simultaneous binding of these two aptamers by combining a structural and dynamics approach. The crystal structure of the ternary complex formed by the thrombin with NU172 and HD22_27mer provides a detailed view of the simultaneous binding of these aptamers to the protein, inspiring the design of novel bivalent thrombin inhibitors. The crystal structure represents the starting model for molecular dynamics study, which points out the cooperation between the binding at the two exosites. In particular, the binding of an aptamer to its exosite reduces the intrinsic flexibility of the other exosite, that preferentially assumes conformations similar to those observed in the bound state, suggesting a predisposition to interact with the other aptamer. This behaviour is reflected in a significant increase of the anticoagulant activity of NU172 when the inactive HD22_27mer is bound to exosite II, providing a clear evidence of the synergic action of the two aptamers.
G4 notes
6 G-tetrads, 2 G4 helices, 2 G4 stems, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.256 type=other  nts=4 GGGG E.DG7,E.DG21,E.DG16,E.DG12
 2 glyco-bond=-s-s sugar=--.- groove=wnwn planarity=0.165 type=other  nts=4 GGGG E.DG8,E.DG20,E.DG17,E.DG11
 3 glyco-bond=-s-s sugar=.3.- groove=wnwn planarity=0.828 type=other  nts=4 GGGG F.DG8,F.DG20,F.DG17,F.DG11
 4 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.254 type=other  nts=4 GGGG G.DG7,G.DG21,G.DG16,G.DG12
 5 glyco-bond=-s-s sugar=--.- groove=wnwn planarity=0.169 type=other  nts=4 GGGG G.DG8,G.DG20,G.DG17,G.DG11
 6 glyco-bond=-s-s sugar=.3.- groove=wnwn planarity=0.841 type=other  nts=4 GGGG I.DG8,I.DG20,I.DG17,I.DG11

List of 2 G4-helices

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG E.DG7,E.DG21,E.DG16,E.DG12
 2  glyco-bond=-s-s sugar=--.- groove=wnwn WC-->Major nts=4 GGGG E.DG8,E.DG20,E.DG17,E.DG11
  step#1  mm(<>,outward)  area=18.39 rise=3.51 twist=15.2
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG E.DG7,E.DG8
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG E.DG21,E.DG20
  strand#3 DNA glyco-bond=s- sugar=-. nts=2 GG E.DG16,E.DG17
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG E.DG12,E.DG11

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG E.DG7,E.DG21,E.DG16,E.DG12
 2  glyco-bond=-s-s sugar=--.- groove=wnwn WC-->Major nts=4 GGGG E.DG8,E.DG20,E.DG17,E.DG11
  step#1  mm(<>,outward)  area=18.39 rise=3.51 twist=15.2

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Helix#2, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG G.DG7,G.DG21,G.DG16,G.DG12
 2  glyco-bond=-s-s sugar=--.- groove=wnwn WC-->Major nts=4 GGGG G.DG8,G.DG20,G.DG17,G.DG11
  step#1  mm(<>,outward)  area=18.39 rise=3.51 twist=15.0
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG G.DG7,G.DG8
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG G.DG21,G.DG20
  strand#3 DNA glyco-bond=s- sugar=-. nts=2 GG G.DG16,G.DG17
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG G.DG12,G.DG11

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG G.DG7,G.DG21,G.DG16,G.DG12
 2  glyco-bond=-s-s sugar=--.- groove=wnwn WC-->Major nts=4 GGGG G.DG8,G.DG20,G.DG17,G.DG11
  step#1  mm(<>,outward)  area=18.39 rise=3.51 twist=15.0

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List of 2 G4-stems

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG E.DG7,E.DG21,E.DG16,E.DG12
 2  glyco-bond=-s-s sugar=--.- groove=wnwn WC-->Major nts=4 GGGG E.DG8,E.DG20,E.DG17,E.DG11
  step#1  mm(<>,outward)  area=18.39 rise=3.51 twist=15.2
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG E.DG7,E.DG8
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG E.DG21,E.DG20
  strand#3  U DNA glyco-bond=s- sugar=-. nts=2 GG E.DG16,E.DG17
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG E.DG12,E.DG11
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT E.DT9,E.DT10
  loop#2 type=lateral   strands=[#4,#3] nts=3 GTA E.DG13,E.DT14,E.DA15
  loop#3 type=lateral   strands=[#3,#2] nts=2 GT E.DG18,E.DT19

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG G.DG7,G.DG21,G.DG16,G.DG12
 2  glyco-bond=-s-s sugar=--.- groove=wnwn WC-->Major nts=4 GGGG G.DG8,G.DG20,G.DG17,G.DG11
  step#1  mm(<>,outward)  area=18.39 rise=3.51 twist=15.0
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG G.DG7,G.DG8
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG G.DG21,G.DG20
  strand#3  U DNA glyco-bond=s- sugar=-. nts=2 GG G.DG16,G.DG17
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG G.DG12,G.DG11
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT G.DT9,G.DT10
  loop#2 type=lateral   strands=[#4,#3] nts=3 GTA G.DG13,G.DT14,G.DA15
  loop#3 type=lateral   strands=[#3,#2] nts=2 GT G.DG18,G.DT19

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List of 6 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#-1 nts=4 GTAG F.DG8,F.DT9,F.DA10,F.DG11
 2 type=lateral   helix=#-1 nts=7 GGGCAGG F.DG11,F.DG12,F.DG13,F.DC14,F.DA15,F.DG16,F.DG17
 3 type=lateral   helix=#-1 nts=4 GTTG F.DG17,F.DT18,F.DT19,F.DG20
 4 type=lateral   helix=#-2 nts=4 GTAG I.DG8,I.DT9,I.DA10,I.DG11
 5 type=lateral   helix=#-2 nts=7 GGGCAGG I.DG11,I.DG12,I.DG13,I.DC14,I.DA15,I.DG16,I.DG17
 6 type=lateral   helix=#-2 nts=4 GTTG I.DG17,I.DT18,I.DT19,I.DG20